Valves are clavate in valve view and cuneate in girdle view. Valves are symmetric to the apical axis. Two distinct groups are currently included within the genus Gomphoneis.
One group contains species (including G. herculeana and G. eriense) with multiseriate striae crossed by longitudinal lines and with stigmata. The longitudinal lines are formed by either marginal lamellae or an axial plate, both internal structures that cover the internal expression of the striae.
The second group contains species (including G. olivacea and G. quadripunctata) that possess multiseriate striae, but the areolae are indistinct under the light microscope. This group lacks longitudinal lines and has a variable number of stigmata, from 0-4. Both groups possess septae and pseudoseptae. The foot pole contains an apical pore field, bisected by the terminal raphe ends.
Cells form mucilaginous stalks, joined together into large colonies. In North America, Gomphoneis is especially diverse in lakes and rivers of midwestern and western states.